Histidine tautomerism-mediated transthyretin amyloidogenesis: A molecular insight.

Characterization of the conformational alterations involved in monomer misfolding is essential for elucidating the molecular basis of the initial stage of protein accumulation. Here, we report the first structural analyses of transthyretin (TTR) (26-57) fragments with two histidine tautomeric states (δ; Nδ1H and ε; Nε2H) using replica-exchange molecular dynamics (REMD) simulations. Explaining the organizational properties and misfolding procedure is challenging because the δ and ε configurations can occur in the free neutral state. REMD revealed that ß-sheet generation is favored for the δδ (16.8%) and εδ (6.7%) tautomeric isomers, showing frequent main-chain contacts between the stable regions near the head (N-terminus) and central (middle) part compared to the εε (4.8%) and δε (2.8%) isomers. The presence of smaller and wider local energy minima may be related to the structural stability and toxicity of δδ/εδ and εε/δε. Histidines31 and 56 were the parts of regular (such as ß-strand) and nonregular (such as coil) secondary structures within the highly toxic TTR isomer. For TTR amyloidosis, focusing on hazardous isomeric forms with high sheet contents may be a potent treatment strategy. Overall, our findings support the tautomerism concept and aid in our comprehension of the basic tautomeric actions of neutral histidine throughout the misfolding process.

Monitoring early-stage ß-amyloid dimer aggregation by histidine site-specific two-dimensional infrared spectroscopy in a simulation study.

Monitoring early-stage ß-amyloid (Aß) dimerization is a formidable challenge for understanding neurological diseases. We compared ß-sheet formation and histidine site-specific two-dimensional infrared (2D IR) spectroscopic signatures of Aß dimers with different histidine states (δ; Nδ1-H, ε; Nε2-H, or π; both protonated). Molecular dynamics (MD) simulations revealed that ß-sheet formation is favored for the δδδ:δδδ and πππ:πππ tautomeric isomers showing strong couplings and frequent contacts between the central hydrophobic core and C-terminus compared with the εεε:εεε isomer. Characteristic blue-shifts in the 2D IR central bands were observed upon monomer-dimer transformation. The εεε:εεε dimer exhibited larger frequency shifts than δδδ:δδδ and πππ:πππ implying that the red-shift may have a correlation with Nδ1-H(δ) protonation. Our results support the tautomerization/protonation hypothesis that attributes Aß misfolding to histidine tautomers as a possible primary initiator for Aß aggregation and facilitates the application of histidine site-specific 2D IR spectroscopy for studying early-stage Aß self-assembly.

Mechanistic Insights into the Polymorphic Associations and Cross-Seeding of Aß and hIAPP in the Presence of Histidine Tautomerism: An All-Atom Molecular Dynamic Study.

Hundreds of millions of people around the world have been affected by Type 2 diabetes (T2D) which is a metabolic disorder. Clinical research has revealed T2D as a possible risk factor for Alzheimer's disease (AD) development (and vice versa). Amyloid-ß (Aß) and human islet amyloid polypeptide are the main pathological species in AD and T2D, respectively. However, the mechanisms by which these two amyloidogenic peptides co-aggregate are largely uninvestigated. Herein, for the first time, we present the cross-seeding between Amylin1-37 and Aß40 considering the particular effect of the histidine tautomerism at atomic resolution applying the all-atom molecular dynamics (MD) simulations for heterodimeric complexes. The results via random seed MD simulations indicated that the Aß40(δδδ) isomer in cross-talking with Islet(ε) and Islet(δ) isomers could retain or increase the ß-sheet content in its structure that may make it more prone to further aggregation and exhibit higher toxicity. The other tautomeric isomers which initially did not have a ß-sheet structure in their monomeric forms did not show any generated ß-sheet, except for one seed of the Islet(ε) and Aß40(εεε) heterodimers complex that displayed a small amount of formed ß-sheet. This computational research may provide a different point of view to examine all possible parameters that may contribute to the development of AD and T2D and provide a better understanding of the pathological link between these two severe diseases.

Molecular mechanism of amyloidogenicity and neurotoxicity of a pro-aggregated tau mutant in the presence of histidine tautomerism via replica-exchange simulation.

The accumulation of ΔK280 tau mutant resulting in neurotoxic oligomeric aggregates is an important but yet mysterious procedure in Alzheimer's disease (AD) development. Recently, we proposed a histidine tautomerization hypothesis of tau fibrillogenesis for the pathobiology of AD and other neuro diseases. However, the influence of neutral histidine tautomeric states on tau mutation is still unclear. Herein, we performed replica-exchange molecular dynamics (REMD) simulations to characterize structural features as well as the mode of toxic action of the ΔK280 tau mutant in the presence of histidine tautomerism. Molecular dynamics (MD) simulation results show that the δε tautomeric isomer (having a distinct global energy minimum) had the highest ß-sheet structure, which adopts a sheet-rich conformer and may have significant influence on the structural behaviors of ΔK280 tau monomers. Furthermore, clustering, residual contact map, mobility and structural analysis exhibited that the presence of ß-strand interactions between stable lysine 8 (K8)-asparagine 13 (N13) and valine 39 (V39)-tyrosine 43 (Y43) residues plus K31-histidine 32 (H32) and K8-N13 (strand-loop-strand [ß-meander] structure) helped δε to form toxic aggregates. Moreover, H299 played a more critical role in the conformational instability of the δε than H268. Overall, the results obtained from this study may be used to arrest neurodegeneration in ΔK280 tau mutation carriers as well as increase the understanding of AD-related tau pathogenesis and strengthen the histidine tautomerism hypothesis of misfolded peptide accumulation.

Impact of A2V Mutation and Histidine Tautomerism on Aß42 Monomer Structures from Atomistic Simulations.

The self-assembly of amyloid-ß (Aß) peptides into senile plaques in the brain is a hallmark of Alzheimer's disease (AD) pathology. Mutation and histidine tautomerism are considered intrinsic origins in the accumulation of Aß. As a first step toward understanding the impact of A2V mutation and histidine tautomerism on the Aß42 isoform, we performed replica-exchange molecular dynamics (REMD) simulations to investigate the effects of histidine tautomerism on the structural properties of A2V Aß42 peptides. There are generally more ß-sheet and less α-helix secondary structures in A2V Aß42 monomers than in WT Aß42, implying a higher aggregation tendency in A2V Aß42, which is consistent with previous studies. The current research will help develop the histidine tautomerism hypothesis of misfolded protein aggregation and eventually elucidate the pathogenesis of AD.

Leveraging attention-enhanced variational autoencoders: Novel approach for investigating latent space of aptamer sequences.

Aptamers are increasingly recognized as potent alternatives to antibodies for diagnostic and therapeutic applications. The application of deep learning, particularly attention-based models, for aptamer (DNA/RNA) sequences is an innovative field. The ongoing advancements in aptamer sequencing technologies coupled with machine learning algorithms have resulted in novel developments. Further research is required to investigate the full potential of deep learning models and address the challenges associated with the generation of sequences, like the large search space of possible sequences. In this study, we propose a workflow that integrates an attention mechanism within a framework of a generative variational autoencoder, to generate novel sequences by expanding latent memory. They show 100 % novelty compared with the dataset, and approximately 88 % of them show negative values for the minimum free energy, which may indicate the likelihood of an RNA sequence folding into a functional structure. Because the field of aptamer discovery is affected by data scarcity, advanced strategies that facilitate the generation of diverse and superior sequences are necessitated. The utilization of our workflow can result in novel aptamers. Thus, investigations such as the present study can address the abovementioned challenge. Our research is anticipated to facilitate further discoveries and advancements in aptamer fields.

Exposure to the electric field: A potential way to block the aggregation of histidine tautomeric isomers of ß-amyloid.

Controlling protein misfolding and accumulation in neurodegeneration is a challenge in chemical neuroscience. The application of appropriate electric fields (EFs) can be a potential noninvasive therapy to treat neuro disorders. The effect of EFs of varying intensities and directions on the conformational dynamics of ß-Amyloid40 (Aß40) under histidine tautomerism has been investigated for the first time. Our findings suggest that peptides tend to align their dipole moments with the orientation of EF. Irrespective of the EF direction, the dipole moment magnitude is affected by the EF strength. With the conformational changes, the EF strength equal to 0.5 V/nm destroyed the ß-sheet content of the δδδ isomer as a potentially toxic agent. The content of the alpha-helical structure which can be transformed into the ß-sheet is reduced. The strength of the EF showed a significant influence on the reduction of the number of intra-protein hydrogen bonds especially when EF is equal to 0.5 V/nm which could facilitate destabilization of the structure of the peptides. Current findings provide quantitative insights into the tautomerization-mediated Aß40 dynamic and conformational changes induced by the external EFs in aqueous solutions, which may provide beneficial information for use as a therapeutic technique.

The use of machine learning modeling, virtual screening, molecular docking, and molecular dynamics simulations to identify potential VEGFR2 kinase inhibitors.

Targeting the signaling pathway of the Vascular endothelial growth factor receptor-2 is a promising approach that has drawn attention in the quest to develop novel anti-cancer drugs and cardiovascular disease treatments. We construct a screening pipeline using machine learning classification integrated with similarity checks of approved drugs to find new inhibitors. The statistical metrics reveal that the random forest approach has slightly better performance. By further similarity screening against several approved drugs, two candidates are selected. Analysis of absorption, distribution, metabolism, excretion, and toxicity, along with molecular docking and dynamics are performed for the two candidates with regorafenib as a reference. The binding energies of molecule1, molecule2, and regorafenib are - 89.1, - 95.3, and - 87.4 (kJ/mol), respectively which suggest candidate compounds have strong binding to the target. Meanwhile, the median lethal dose and maximum tolerated dose for regorafenib, molecule1, and molecule2 are predicted to be 800, 1600, and 393 mg/kg, and 0.257, 0.527, and 0.428 log mg/kg/day, respectively. Also, the inhibitory activity of these compounds is predicted to be 7.23 and 7.31, which is comparable with the activity of pazopanib and sorafenib drugs. In light of these findings, the two compounds could be further investigated as potential candidates for anti-angiogenesis therapy.

Histidine Tautomerism Driving Human Islet Amyloid Polypeptide Aggregation in the Early Stages of Diabetes Mellitus Progression: Insight at the Atomistic Level.

Early oligomerization of human islet amyloid polypeptide (hIAPP), which is accountable for ß-cell death, has been implicated in the progression of type 2 diabetes mellitus. Some researches have shown the connection between hIAPP and Alzheimer's disease as well. However, the mechanism of peptide accumulation and associated cytotoxicity remains unclear. Due to the unique properties and significant role of histidine in protein sequences, here for the first time, the tautomeric effect of histidine at the early stages of amylin misfolding was investigated via molecular dynamics simulations. Considering Tau and Pi tautomeric forms of histidine (Tau and Pi tautomers are denoted as ϵ and δ, respectively), simulations were performed on two possible isomers of amylin. Our analysis revealed a higher probability of transient α-helix generation in the δ isomer in monomeric form. In dimeric forms, the δδ and δϵ conformations showed an elevated amount of α-helix and lower coil in comparison to the ϵϵ dimer. Due to the significant role of α-helix in membrane disruption and transition to ß-sheet structure, these results may imply a noticeable contribution of the δ isomer and the δδ and δϵ dimers rather than ϵ and ϵϵ conformations in the early stages of diabetes initiation. Our results may aid in elucidating the hIAPP self-association process in the etiology of amyloidosis.

Unraveling the Histidine Tautomerism Effect on the Initial Stages of Prion Misfolding: New Insights from a Computational Perspective.

The aggregation and structural conversion of normal prion peptide (PrPC) into the pathogenic scrapie form (PrPSc), which can act as a seed to enhance prion amyloid fiber formation, is believed to be a crucial event in prionopathies. Previous research suggests that the prion monomer may play an important role in oligomer generation during disease pathogenesis. In the present study, extensive replica-exchange molecular dynamics (REMD) simulations were conducted to explore the conformational characteristics of the huPrP (125-160) monomer under the histidine tautomerism effect. Investigating the structural characteristics and fibrilization process is challenging because two histidine tautomers [Nε2-H (ε) and Nδ1-H (δ)] can occur in the open neutral state. Molecular dynamics (MD) simulation outcomes have shown that the toxic εδ and δδ isomer (containing several and broader local minima) had the highest α-helix structures, with contents of 21.11% and 21.01%, respectively, and may have a strong influence on the organizational behavior of a monomeric prion. The amino acids aspartate 20 (D20)-asparagine 29 (N29) and isoleucine 15 (I15)-histidine 16 (H16), D20-arginine 27 (R27) as well as N29 formed α-helix with the highest probabilities in the δδ and εδ isomer, accordingly. On the basis of our findings, we propose the histidine tautomerization hypothesis as a new prion accumulation mechanism, which may exist to induce the formation of prion accumulates. Overall, our tautomerism hypothesis constitutes a promising perspective for enhancing understanding of prion disease pathobiology and may help in the design of a good inhibitor.

Molecular insight into the early stage of amyloid-ß(1-42) Homodimers aggregation influenced by histidine tautomerism.

Aggregated amyloid ß-peptide (Aß) in small oligomeric forms inside the brain causes synaptic function disruption and the development of Alzheimer's disease (AD). Histidine is an important amino acid that may lead to structural changes. Aß42 monomer chain includes 3 histidine residues that considering two ε and δ tautomers 8 isomers, including (εεε) and (εδδ) could be formed. Molecular dynamics simulation on homodimerization of (εεε) (the most common type of tautomers) and (εδδ) tautomers with different initial configurations using monomer chains from our previous work were performed to uncover the tautomeric behavior of histidine on Aß42 aggregation in a physiological pH which is still largely unknown and impossible to observe experimentally. We found a higher propensity of forming ß-sheet in (εδδ) homodimers and specifically in a greater amount from Aß42 than from Aß40. A smaller amount of ß-sheet formation was observed for (εεε) homodimers compared with (εδδ). Additionally, interactions in (εδδ) homodimers may indicate the importance of the hydrophobic core and C-/N-terminals during oligomerization. Our findings indicate the important role of the tautomeric effect of histidine and (εδδ) homodimers at the early stage of Aß aggregation.

Insights into amyotrophic lateral sclerosis linked Pro525Arg mutation in the fused in sarcoma protein through in silico analysis and molecular dynamics simulation.

A novel heterozygous mutation, Pro525Arg (P525R) in the Fused in Sarcoma (FUS) protein is predominant in young adult females with familial amyotrophic lateral sclerosis (fALS). Investigation of the biophysical characteristics of this mutation through analysis of protein conformation could provide insights into the pathogenic mechanism of amyotrophic lateral sclerosis (ALS). Here, several computational prediction tools were applied to investigate the effect of P525R on the stability, flexibility, and function of FUS. Conservation and biochemical analyses showed that P525 is highly conserved; the mutation of proline to arginine at position 525 in FUS results in a notable increase in molecular weight, number of hydrogen bonds, and loss of hydrophobicity. By performing electrostatic potential, intra-protein interaction, and binding affinity analyses, we found increased electrostatic potential charge in the mutant protein and fewer hydrophobic interactions than the wild-type structure. Binding affinity of the FUS nuclear localization signal (NLS) mutant for transportin (Trn1) was also decreased compared to wild-type. Our molecular dynamics (MD) simulation results highlighted the exchange between hydrophobic and hydrophilic residues from the core to the surface in the mutant structure; also, upon P525R mutation, FUS became less stable, less flexible and more compact and rigid. Overall, this study demonstrated that the Pro525Arg mutation significantly alters the structure and conformation of FUS through loss of nuclear function, thereby likely contributing to its accumulation in the cytoplasm, which has been implicated in the pathogenesis of fALS. Our study can potentially aid in the design of drugs for FUS-associated neurodegenerative diseases.

Intrinsic Origin of Tau Protein Aggregation: Effects of Histidine Tautomerism on Tau267-312 Monomer.

Histidine tautomerism is considered a crucial component that affects the constitutional and accumulation characteristics of the tau267-312 monomer in the neutral condition, which are connected with the pathobiology of Alzheimer's disease (AD). Interpreting the organizational characteristics and accumulation procedure is a challenging task because two tautomeric conformations (the Nε-H or Nδ-H tautomer) can occur in the open neutral condition. In the current work, replica-exchange molecular dynamics (REMD) simulations were performed to investigate the structural properties of the tau267-312 monomer considering the histidine tautomeric effect. Based on the simulation outcomes, the histidine 268 (H268) (δ)-H299 (δ) (δδ) isomer had the highest ß-sheet content with a value of 26.2%, which acquires a sheet-governing toxic conformer with the first abundant conformational state of 22.6%. In addition, δδ displayed notable antiparallel ß-sheets between lysine 8 (K8)-asparagine 13 (N13) and valine 40 (V40)-tyrosine 44 (Y44) as well as between K32-H33 and V40-Y44 (ß-meander supersecondary structure), indicating this tautomeric isomer may exist to stimulate tau oligomerization. Furthermore, H299 was found to play an essential role in the structural stabilization of the δδ isomer compared with H268. The present research will aid in obtaining insight into the organizational and accumulation properties of tau protein in the presence of histidine tautomerism to control AD.

Intrinsic Origin of Amyloid Aggregation: Collective Effects of the Mutation and Tautomerism of Histidine.

Mutation is considered an important factor in the accumulation of amyloid-ß (Aß), which is a hallmark of Alzheimer's disease (AD). A2V Aß40 shows a higher aggregation tendency; however, the existing knowledge is not sufficient to explain the mechanism. We performed replica-exchange molecular dynamics simulations (REMD) to investigate the structural properties of A2V Aß40 monomers and consider the tautomerism of histidine. The collective effects of the mutation and tautomerism leads A2V Aß40 to much higher ß-sheet and lower α-helix contents than WT Aß40, which may explain the enhanced aggregation kinetics of A2V Aß40 with respect to WT Aß40. The current research provides new insights on understanding the pathology of AD.

Intrinsic origin of amyloid aggregation: Behavior of histidine (εεε) and (δδδ) tautomer homodimers of Aß (1-40).

Amyloid-beta protein (Aß) accumulation in the brain, which is influenced by several factors, is a hallmark of Alzheimer's disease (AD). Despite the important role of histidine in stabilizing the fibrillar structure of the Aß peptide at neutral pH, the effect of histidine tautomerism on Aß peptide aggregation is still largely unknown. Histidine is in equilibrium between δ and ε tautomers and there are three histidine residues (H6, H13, and H14) in the Aß(1-40) peptide. We performed molecular dynamics simulation on (δδδ) and (εεε) histidine tautomers with different initial homodimeric configurations to elucidate structural and aggregation features. Results indicate that (εεε) homodimers have very low propensity or almost no tendency to form ß-sheets, whereas (δδδ) dimers predominantly form ß-sheets due to interactions between central hydrophobic core (CHC) residues and C-terminal residues. ß-sheet formation occurred in the same regions of each dimer chain at the CHC and C-/N- terminals for different configurations of (δδδ). These results suggest that (δδδ) has an important role in AD progression. Our study provides deeper insight into the effect of tautomerism of histidine residues in Aß(1-40) on amyloid aggregation.

Monoamine oxidase-A targeting probe for prostate cancer imaging and inhibition of metastasis.

Mitochondrial enzyme monoamine oxidase (MAO-A) is known to be overexpressed in prostate cancer (PCa) cells. Herein, we have developed a two-photon probe (PCP-1) for selectively targeting and imaging the MAO-A in PCa. Supported by enzymatic docking and in vitro experiments, PCP-1 showed efficiency to visualize MAO-A overexpressing cells and inhibit their growth and metastasis potential.